Biochem Mod 3

CHAPTER 13

metabolites

intermediate or end product of cellular metabolism

catabolism

the degradative phase of metabolism (release energy, makes ATP equivalents)

anabolism (biosynthesis)

the building phase of metabolism (requires energy, spends ATP and equivalents)

change in free energy (ΔG)

spontaneity of the rxn

independent of the pathway

exergonic rxn

-ΔG — free energy is released

endergonic reaction

+ΔG — free energy is gained

Enthalpy (H)

the heat content of the reacting system (reflecting changed in covalent and non covalent bonds between reactants and products)

exothermic

-ΔH — heat is released

endothermic

+ΔH — heat is absorbed

Entropy (S)

the randomness or disorder in a system

-ΔS

reactants are less complex and more disordered

+ΔS

product are less complex and more disordered

thermodynamics of living cells

cells produce order within themselves by generating more disorder in their surroundings

living organisms take free energy from, and return heat entropy to, their surroundings

standard biochemical conditions (ΔG’^o)

25^oC

1 atm

when pH=7, [H₂O] = 55.5 M, [Mg²⁺] = 1 mM

homolytic cleavage

each atom leaves the bond as a radical, carrying one unpaired electron

heterolytic cleavage

(more common) one atom retains both bonding electrons

nucleophiles

e- rich in and capable of donating electrons

electrophiles

electron deficient and seek electrons

• often polar double bonds (like carbonyls, imines, and phosphates)

carbonyl chemistry

carbonyl carbon is electrophilic

the α carbon of carbonyl is acidic and nucleophilic

3 common reactions to form and break carbon carbon bonds

1. aldol condensation

2. claisen condensation

3. decarboxylation reactions

group transfer reactions

• Convert acyl groups from one heteroatom to another

• transfer glycosyl groups through nucleophilic substitution at C-1 of a sugar ring (via an S_N1 or S_N2 pathway)

• transfer phosphates

Phosphate and ADP make excellent _______ _______.

leaving groups

hydrolysis of phosphoanhydride bond in ATP

releases a lot of free energy because…

• relieves internal electrostatic repulsion in ATP

• phosphate is stabilized by alternate resonance forms

ATP —> ADP + P_i ΔG'^o value

-30.5

phosphoenolpyruvate

tautomerization of the enol product to the more stable keto form drives hydrolysis (-ΔG’^o)

1, 3-bisphosphoglycerate (BPG)

formation of an ion favors forming 3-phosphoglycerate, which is also stabilized by its resonance form (-ΔG’^o)

acetyl-coenzyme A (carbohydrate and fatty acid intermediate)

thioesters have less resonance stabilization than esters, so the hydrolysis makes and ion and allows more resonance (-ΔG’^o)

phosphocreatine (secondary high-energy molecule found in muscle, heart, brain)

hydrolysis provides resonance stabilization of creatine (-ΔG’^o)

“high-energy” compounds

(-ΔG’^o) more negative than -25 kJ/mol

“low-energy” compounds

(-ΔG’^o) less negative than -25 kJ/mol

adenylation

most thermodynamically favored rxns (nucleophilic attack at α phosphate)

• PP_i formed as byproduct

  • Hydrolyzed by two P_i by inorganics pyrophosphatase, releasing additional energy

electron flow in oxidation-reduction reactions

metabolic intermediates

• electron carried

• acceptors with higher electron affinities

OIL RIG

oxidation is loss

• Loss of electrons

reduction is gain

• gain of electrons

electromotive force (emf, ΔE)

proportional to the difference in electron affinity between chemical species

dehydrogenation

a compound loses two electrons and two hydrogen ions

• catalyzed by dehydrogenases

these reactions can transfer electrons…

• directly as e-

• as hydrogen atoms

• as hydride ion (H-)

• through direct combination with oxygen

the nerst equation (relation not equation

relates the reduction potential (E) to the standard reduction potential (E^o)

NAD and NADP

water-soluble coenzymes that undergo reversible oxidation and reduction in many of the electron-transfer reactions

niacin

the vitamin form of NAD and NADP

pellagra

dietary deficiency of niacin prevents NAD synthesis and causes this\

• Four D’s: dermatitis, diarrhea, dementia, death

flavoproteins

enzymes that catalyze oxidation-reduction reactions using flavins

• either flavin mononucleotide (FMN) or flavin adenine dinucleotide (FAD) as coenzyme

• may be names either dehydrogenases or oxidoreductases

flavin molecules

coenzymes derived from the vitamin riboflavin

• reduction potentials depend on the flavoprotein with which they are associated

• can accept either one or two electrons in the form of one or two hydrogen atoms from reduced substrate

Chap 14

glycolysis

ten-enzyme catalyzed reactions to convert glucose to yield two molecules of three-carbon compound pyruvate

• glucose only partially oxidized in this process, but free energy is conserved as ATP and NADH

catabolism

a set of metabolic pathways that breaks down larger molecules into smaller units with energy release

cellular respiration

the process of cells converting the chemical energy from nutrients into ATP

= oxidation of biological fuels in the presence of O₂ to produce ATP

cellular respiration step

1. glycolysis

2. pyruvate oxidation

3. Citric Acid (Krebs) Cycle

4. Oxidative phosphorylation

location of glycolysis

cytosol

location of cellular respiration (not glycolysis)

mitocondria

preparatory phase of glycolysis (1)

ATP is consumed

hexose carbon is converted to 2x glyceraldehyde 3-phosphate (G3P)

payoff phase of glycolysis (2)

2 ATP and 2 NADH is generated

yields two pyruvate (Pyr)

• each step occurs twice per glucose molecule (glucose 6C splits into 2 G3P 3C - each G3P goes through independently)

fermentation

metabolism that breaks down and extracts energy from molecules but does NOT consume oxygen

gluconeogenesis

the pathway that converts pyruvate (and intermediates) to glucose

Glycolysis Rxn 1 Hexokinase (HK)

• Phosphorylate C-6 of D-Glucose

• attacks γ (furthest) phosphate of ATP, generating ADP

Glucose —> Glucose 6-phosphate

Glycolysis Rxn 2 Phosphohexose Isomerase (PHI)

• catalyzes the reversible isomerization of G6P and F6P

• phosphorylate each terminal carbon

Glycolysis Rxn 3 Phosphofructokinase-1 (PFK-1)

• installs second phosphoryl group from ATP to F6P to yield fructose 1,6-bisphosphate

• Now phosphoryl group on each end of the sugar

Glycolysis Rxn 4 Aldolase

• catalyzes a reverse aldol condensation

• cleaves F1,6BP to yield glyceraldehyde 3-phosphate (G3P) and dihydroxyacetone (DHAP)

generates the 2x three carbon sugars

“Schiff Base” intermediate

an imine formed from a lysine and a carbonyl (seen in Glycolysis Rxn 4)

Glycolysis Rxn 5 Triose Phosphate Isomerase (TPI)

• converts DHAP to G3P

• final step of preperatory process

Glycolysis Rxn 6 Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDH)

• catalyzes oxidation G3P to 1,3BPG

• NAD is reduced while the aldehyde is oxidized and coupled to inorganic phosphate

first step in payoff phase

Glycolysis Rxn 7 Phosphoglycerate Kinase (PGK)

• transfers the high energy phosphoryl group from the carboxyl group of 1,3BPG to ADP, forming ATP and 3PG

Rxn is named in the reverse rxn, but it is favorable in the forward direction

kinase

transfers Pi from ATP

substrate-level phosphorylation

the formation of ATP by phosphoryl group transfer from a substrate to ADP

• tb def: direct synthesis of ATP from ADP using a high-E intermediate, without involving an electron transport chain or oxygen

Glycolysis Rxn 8 Phosphoglycerate Mutase (PGM)

catalyzes a reversible shift of the phosphoryl group between C2 and C3 of the glycerate

• rxn sets up the enol formation that come in the next step so glycolysis can make a second ATP from substrate level phosphorylation

Glycolysis Rxn 9 Enolase (ENO)

promotes reversible removal of a molecule of water from 2PG to yield phosphoenolpyruvate (PEP)

• enzyme contains 2 Mg2+ ions to bind the phosphate and stabilize the enolic intermediate

Glycolysis Rxn 10 pyruvate kinase (PK)

catalyzes the transfer of the phosphoryl group from PEP to ADP, yielding pyruvate

• second substrate-level phosphorylation and also named for reverse rxn